Even if a system is not well equilibrated (but not so far from
equilibrium) ,energy should be conserved in NVE ensemble.
Try to lower the nstlist from 10 to 1 i.e. renew every time the
neighbourlist. In systems I have studied, that is the key that improve
much more energy conservation. It works even without switching of VdW
potential.
Luca Dre Gaetani
Message: 1
Date: Thu, 12 Mar 2009 13:59:11 +1100
From: Mark Abraham <mark.abra...@anu.edu.au>
Subject: Re: [gmx-users] Re: Energy Drift in Gromacs 4.0
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <49b87a7f.30...@anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Ilya Chorny wrote:
If I plot the K.E(t) and P.E.(t) they are both going down. In an NVE
simulation they should counter balance. I am leaking K.E. somewhere. I
reran with a relaxed P.E(t) and saw the same behavior. This is
happening both at 2 and 4 fs so its not a time step issue. Any thoughts?
I thought it might be COM removal so I turned it off to no avail.
"going down" is seriously unhelpful. I told you you needed to
equilibrate before measuring such things. If you want people to take
your problem seriously, you'll need to announce that you have
equilibrated and for how long and in what ensembles, etc. If you're
having a problem, you need to demonstrate what areas you feel are not
causing it. We're not your family doctor who will ask a pile of
questions to find out the problem :-)
Mark
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